RetrogeneDB ID: retro_ptro_1851

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:190828521..190829081(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PSMD10
• Ensembl ID: ENSPTRG00000022169
• Aliases: None
• Description: None

Sequence

>retro_ptro_1851
ATGGAGGGGTGTGTGTCTAACCTAATGGTCTGCAACCTGGCCTACAGAGGAAGCTGGAAGAGTTGAAGGAGAGTATTCTG
GCAGATAAATTCCTATCTAGTAAAACTGACTAGAACAGCAGAACTGCATTGCACTGGGCATGCTCAGCCAGACATGCAGA
AATTGTTGAATTTGTGTTGCAACTTGGAGTGCCAGTGAGTGATAAAGGCGATACAGGTTGGTCTCCTCTTCATACTGTGG
CTTCCGCTGGGCGGGATGAGATTGTAAAAGCCCTTCTGGGAAAATGTGCTCAAGTAAATGCTGTCAGTCAAAATGGCTGT
ACTCCCCTACATTATACAGCTTCCAAAAACAGGAATGAGATTGTTGTCAAGTTACTAGAAGGCGGGGTTGATCCACATGC
TGAGGACCATTGTGAGGCTACAGCAATGCACCGGGCAGCAGCCAAGGGTAACTTGAAGATGATTCCTATCCTTCTGTACT
ACAGAACATCCACAAACATCCAAGACACTGAGGGTAACACTCCTCTACACTTAGCCTGTGATGAGGAGAGAGTGGAAGAA

Alignment

ORF - retro_ptro_1851 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.04 %
• Parental protein coverage: 82.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGCVSNLMVCNLAYSG-KLEELKESILADKSLATRTDQDSRTALHWACSAGHTEIVEFLLQLGVPVNDK
          MEGCVSNLMVCNLAY.G.KLEELKESILADK.L...TD..SRTALHWACSA.H.EIVEF.LQLGVPV.DK
Retrocopy MEGCVSNLMVCNLAYRG<KLEELKESILADKFLSSKTD*NSRTALHWACSARHAEIVEFVLQLGVPVSDK

Parental  DDAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDHYE
          .D.GWSPLH..ASAGRDEIVKALLGK.AQVNAV.QNGCTPLHY.ASKNR.EI.V.LLEGG..P.A.DH.E
Retrocopy GDTGWSPLHTVASAGRDEIVKALLGKCAQVNAVSQNGCTPLHYTASKNRNEIVVKLLEGGVDPHAEDHCE

Parental  ATAMHRAAAKGNLKMIHILLYYKASTNIQDTEGNTPLHLACDEERVEE
          ATAMHRAAAKGNLKMI.ILLYY..STNIQDTEGNTPLHLACDEERVEE
Retrocopy ATAMHRAAAKGNLKMIPILLYYRTSTNIQDTEGNTPLHLACDEERVEE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	21.68 RPM
SRP007412_cerebellum	0.00 RPM	29.54 RPM
SRP007412_heart	0.00 RPM	10.14 RPM
SRP007412_kidney	0.00 RPM	20.48 RPM
SRP007412_liver	0.03 RPM	15.02 RPM
SRP007412_testis	2.42 RPM	21.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1851 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1851 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1851 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2737
Gorilla gorilla	retro_ggor_1906
Pongo abelii	retro_pabe_2275

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012006	1 retrocopy	retro_acar_134,
Callithrix jacchus	ENSCJAG00000007717	1 retrocopy	retro_cjac_2515,
Cavia porcellus	ENSCPOG00000015068	1 retrocopy	retro_cpor_358,
Dasypus novemcinctus	ENSDNOG00000001902	5 retrocopies	retro_dnov_1194, retro_dnov_208, retro_dnov_705, retro_dnov_824, retro_dnov_835,
Homo sapiens	ENSG00000101843	3 retrocopies	retro_hsap_1214, retro_hsap_2435, retro_hsap_2737,
Gorilla gorilla	ENSGGOG00000002969	3 retrocopies	retro_ggor_1515, retro_ggor_1906, retro_ggor_945,
Macaca mulatta	ENSMMUG00000016981	1 retrocopy	retro_mmul_1290,
Nomascus leucogenys	ENSNLEG00000014001	2 retrocopies	retro_nleu_243, retro_nleu_690,
Oryctolagus cuniculus	ENSOCUG00000010837	1 retrocopy	retro_ocun_793,
Otolemur garnettii	ENSOGAG00000006419	1 retrocopy	retro_ogar_213,
Procavia capensis	ENSPCAG00000005221	1 retrocopy	retro_pcap_461,
Pongo abelii	ENSPPYG00000020618	3 retrocopies	retro_pabe_1010, retro_pabe_1793, retro_pabe_2275,
Pan troglodytes	ENSPTRG00000022169	3 retrocopies	retro_ptro_1407, retro_ptro_1851 , retro_ptro_831,
Ictidomys tridecemlineatus	ENSSTOG00000003783	3 retrocopies	retro_itri_1684, retro_itri_312, retro_itri_676,
Tarsius syrichta	ENSTSYG00000009920	13 retrocopies	retro_tsyr_1160, retro_tsyr_1674, retro_tsyr_1684, retro_tsyr_1741, retro_tsyr_1830, retro_tsyr_1968, retro_tsyr_1989, retro_tsyr_2010, retro_tsyr_2138, retro_tsyr_2151, retro_tsyr_2167, retro_tsyr_674, retro_tsyr_803,